Scope of work for Stanford University Stanford University has a world-renowned expertise in microarray technology and research using microarrays. As part of this expertise, Stanford has built the Stanford Microarray Database (SMD), the largest academic microarray database in the world, and has created the Stanford Functional Genomics Facility (SFGF), which manufactures high quality, high density microarrays for many different organisms, and provides researchers with additional services to help them perform high quality research. We propose a core facility for the Region IX Regional Center of Excellence (RCE) in Emerging Infectious Diseases and Biodefense that marries these two components, SMD and SFGF, to provide all researchers in the Center with a complete microarray solution, including array manufacture, databasing and sharing of raw and processed data, data analysis and data dissemination and publication. This core will provide services for the design of new microarrays, the ability to include probes for host and pathogen organisms on the same array, and services to manufacture those arrays. The microarray database will be populated with the most current sets of gene annotation for each of the organisms whose genes are represented on the microarrays used by members of the RCE, and we will update these data as new annotation becomes available. We will also provide extensive user support to members of the RCE, in the form of e-mail and phone support, as well as organizing tutorials on how to use the database and analyze microarray data. Finally, we will develop new algorithms, and write additional software tools implementing those algorithms, that will be specifically directed towards the analysis of microarray data generated from both host and pathogen simultaneously. In this way, these tools will be able to be used to dissect the host's response to the pathogen, and identify how the pathogen in turn reacts to that response.